Afro-Derived Amazonian Populations: Inferring Continental Ancestry and Population Substructure

A panel of Ancestry Informative Markers (AIMs) was used to identify population substructure and estimate individual and overall interethnic admixture in 294 individuals from seven African-derived communities of the Brazilian Amazon. A panel of 48 biallelic markers, representing the insertion (IN) or the deletion (DEL) of small DNA fragments, was employed for this purpose. Overall interethnic admixture estimates showed high miscegenation with other ethnic groups in all populations (between 46% and 64%). The proportion of ancestral genes varied significantly among individuals of the sample: the contribution of African genes varied between 12% and 75%; of European genes between 10% and 73%; and of Amerindians genes between 8% and 66%. The obtained data reveal a high contribution of Amerindian genes in these communities, unlike in other African-derived communities of the Northeast and the South of Brazil. In addition, the majority of the Amerindian contribution may result from the preferential inclusion of indigenous women in the African descent groups. High heterogeneity of the proportion of interethnic admixture among analyzed individuals was found when the proportion of ancestral genes of each individual of the sample was estimated. This heterogeneity is reflected in the fact that four populations can be considered as substructured and that the global African descent sample is possibly formed by two subpopulations

Extracting Food Substitutes From Food Diary via Distributional Similarity

Genetic ancestry admixture of patients infected with Influenza A(H1N1)pdm09 sorted by African ancestry. Each individual ancestry is depicted as a column, whereas color represents the proportion of ancestry estimated for that individual (African = blue; European = brown; Native American = green). (A) Non-hospitalized patients and (B) Hospitalized patients

Allelic frequencies and statistical data obtained from 12 codis STR loci in an admixed population of the Brazilian Amazon

The allelic frequencies of 12 short tandem repeat loci were obtained from a sample of 307 unrelated individuals living in Macapá, a city in the northern Amazon region, Brazil. These loci are the most commonly used in forensics and paternity testing. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 46%, 35% and 19%. Comparing these allele frequencies with those of other Brazilian populations and of the Iberian Peninsula population, no significant distances were observed. The interpopulation genetic distances (FST coefficients) to the present database ranged from FST = 0.0016 between Macapá and Belém to FST = 0.0036 between Macapá and the Iberian Peninsula

Autosomal STR Analyses in Native Amazonian Tribes Suggest a Population Structure Driven by Isolation by Distance

Eleven short tandem repeat loci (CSF1P0, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, TH01, and TPOX) were investigated in 232 individuals from 6 Amazonian native tribes (Tiriyó, Wai˜api, Zoé, Urubu-Kaapor, Awa-Guajá, and Parakan˜a). We added the new data to a database that included five previously typed native populations from the same area (Wai Wai, Gavi˜ao, Zoró, Suruí, and Xavante). The results presented here concern this new data set, which accounts for 526 individuals in total. We tested whether major geographic or linguistic barriers to gene flow exist among such human groups and tried to find a possible anthropological or ethnological explanation for such patterns. We measured the average heterozygosity (H) and the number of alleles (NA) and found that both are lower than values observed in populations of different ethnic backgrounds, such as European or African descendants. Despite such a result, we found high between-population variation; lower H and/or NA values were obtained from four isolated tribes that came into contact with external nonnative populations in recent times (1921–1989). By applying analysis of molecular variance, generalized hierarchical modeling, and the Structure Bayesian analysis, we were not able to detect any significant geographic or linguistic barrier to gene flow. Geographic autocorrelation analysis suggests that the genetic structure of native Amazonian tribes is better explained by isolation by distance because the level of genetic similarity decreases according to linear geographic distance, reaching null or negative values at a scale of 300 km

Single locus and haplotype genetic diversities calculated for the 5 different regions as well as in the total sample from Brazil.

<p>Single locus and haplotype genetic diversities calculated for the 5 different regions as well as in the total sample from Brazil.</p

Probability of finding at least one mutation between two Y-STR haplotypes one to four generations apart.

*<p>Single locus mutation rates are according to YHRD (<a href="http://www.yhrd.org" target="_blank">www.yhrd.org</a>) and Ballantyne et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040007#pone.0040007-Ballantyne2" target="_blank">[35]</a>; haplotype mutation rates for the different sets have been calculated as the average mutation of the corresponding.</p

Map of Brazil indicating the geographical location of the 17 different sampling places located in 5 geopolitical regions.

<p>Map of Brazil indicating the geographical location of the 17 different sampling places located in 5 geopolitical regions.</p

MDS plot based on the pairwise R_ST genetic distance matrix (Stress = 0.134).

<p>MDS plot based on the pairwise R_ST genetic distance matrix (Stress = 0.134).</p

Assessing Interethnic Admixture Using an X-Linked Insertion-Deletion Multiplex

In this study, a PCR multiplex was optimized, allowing the simultaneous analysis of 13 X-chromosome Insertion/deletion polymorphisms (INDELs). Genetic variation observed in Africans, Europeans, and Native Americans reveals high inter-population variability. The estimated proportions of X-chromosomes in an admixed population from the Brazilian Amazon region show a predominant Amerindian contribution (congruent to 41%), followed by European (congruent to 32%) and African (congruent to 27%) contributions. The proportion of Amerindian contribution based on X-linked data is similar to the expected value based on mtDNA and Y-chromosome information. The accuracy for assessing interethnic admixture, and the high differentiation between African, European, and Native American populations, demonstrates the suitability of this INDEL set to measure ancestry proportions in three-hybrid populations, as it is the case of Latin American populations. Am. J. Hum. Biol. 21:707-709, 2009. (C) 2009 Wiley-Liss, Inc.Fundacao para a Ciencia e a Tecnologia (FCT)[SFRH/BD/30039/2006]Milenio/CNPq (Conselho Nacional de Desenvolvimento Cientifico, e Tecnologico)FINEP (Financiadora de Estudos e Projetos)UFPA (Universidade Federal do Para